Functional analysis of anionic phospholipids in cell metabolism in {\it Escherichia coli\/}

The major goal of this work was to understand the function of anionic phospholipid in E. coli cell metabolism. One important finding from this work is the requirement of anionic phospholipid for the DnaA protein-dependent initiation of DNA replication. An rnhA mutation, which bypasses the need for the DnaA protein through induction of constitutive stable DNA replication, suppressed the growth arrest phenotype of a $pgsA$ mutant in which the synthesis of anionic phospholipid was blocked. The maintenance of plasmids dependent on an $oriC$ site for replication, and therefore DnaA protein, was also compromised under conditions of limiting anionic phospholipid synthesis. These results provide support for the involvement of anionic phospholipids in normal initiation of DNA replication at oriC in vivo by the DnaA protein. In addition, structural and functional requirements of two major anionic phospholipids, phosphatidylglycerol and cardiolipin, were examined. Introduction into cells of the ability to make phosphatidylinositol did not suppress the need for the naturally occurring phosphatidylglycerol. The requirement for phosphatidylglycerol was concluded to be more than maintenance of the proper membrane surface charge. Examination of the role of cardiolipin revealed its ability to replace the zwitterionic phospholipid, phosphatidylethanolamine, in maintaining an optimal membrane lipid organization. This work also reported the DNA sequence of the cls gene, which encodes the CL synthase responsible for the synthesis of cardiolipin. ^

A Ladder Operator Solution to the Particle in a Box Problem

A ladder operator solution to the particle in a box problem of elementary quantum mechanics is presented, although the pedagogical use of this method for this problem is questioned.

Advance P. Chem. Problems (I) Populations, Partition Functions, Particle in Box, Harmonic Oscillators, Angular Momentum and Rigid Rotor

This is a set of P. Chem. problems posed at slightly higher than the normal text book level, for students who are continuing in the study of this subject.

The Role of Raf Kinase Inhibitor Protein in Cell Motility

Raf Kinase Inhibitor Protein (RKIP) has been identified as a phosphatidylethanolamine-binding protein capable of inhibiting Raf-1 kinase, an enzyme significant in cell proliferation and cancer development. When properly functioning, RKIP can mediate the expression of Raf-1 kinase and help prevent uncontrolled cell division. RKIP also has suggested, but unclear, roles in spindle fiber formation during mitosis, regulation of apoptosis, and cell motility. The Fenteany laboratory in the Chemistry Department identified a new small molecule, named Locostatin, as a cell migration inhibitor in mammalian cells, with RKIP as its primary molecular target. Dictyostelium discoideum possess two RKIP proteins, RKIP-A and RKIP-B. In order to begin to study the function of RKIP in D. discoideum and its role in cell motility, I created a mutant cell line which lacks a functional RKIP-A gene. In this paper, we show that removal of RKIP-A does not affect vegetative motility, but impairs chemotaxis and development in the presence of drug. Interestingly, RKIP-A knockout mutants appear more resistant to drug effects on vegetative motility than wild-type cells. More research is needed to reconcile these seemingly contrasting results, and to better develop a model for RKIP-A’s role in cell motility.

Analysis of the E1-ubiquitin activating enzyme, Uba1, in cell death and tissue growth in Drosophila

Ubiquitination is an essential process involved in basic biological processes such as the cell cycle and cell death. Ubiquitination is initiated by ubiquitin-activating enzymes (E1), which activate and transfer ubiquitin to ubiquitin-conjugating enzymes (E2). Subsequently, ubiquitin is transferred to target proteins via ubiquitin ligases (E3). Defects in ubiquitin conjugation have been implicated in several forms of malignancy, the pathogenesis of several genetic diseases, immune surveillance/viral pathogenesis, and the pathology of muscle wasting. However, the consequences of partial or complete loss of ubiquitin conjugation in multi-cellular organisms are not well understood. Here, we report the characterization of nba1, the sole E1 in Drosophila. We have determined that weak and strong nba1 alleluias behave genetically different and sometimes in opposing phenotypes. For example, weak uba1 alleluias protect cells from cell death whereas cells containing strong loss-of-function alleluias are highly apoptotic. These opposing phenotypes are due to differing sensitivities of cell death pathway components to ubiquitination level alterations. In addition, strong uba1 alleluias induce cell cycle arrest due to defects in the protein degradation of Cyclins. Surprisingly, clones of strong uba1 mutant alleluias stimulate neighboring wild-type tissue to undergo cell division in a non-autonomous manner resulting in severe overgrowth phenotypes in the mosaic fly. I have determined that the observed overgrowth phenotypes were due to a failure to downregulate the Notch signaling pathway in nba1 mutant cells. Aberrant Notch signaling results in the secretion of a local cytokine and activation of JAK/STAT pathway in neighboring cells. In addition, we elucidated a model describing the regulation of the caspase Dronc in surviving cells. Binding of Dronc by its inhibitor Diap1 is necessary but not sufficient to inhibit Dronc function. Ubiquitin conjugation and Uba1 function is necessary for the negative regulation of Dronc. ^

Alterations in cell adhesion and migration are transcriptionally regulated by the tumor suppressor, TP53

The p53 transcription factor is a tumor suppressor and a master regulator of apoptosis and the cell cycle in response to cell stress. In some advanced tumors, such as prostate cancers, the loss of p53 correlates with an increase in the occurrence of metastases. In addition, several groups have suggested that p53 status correlates with changes in cell migration and cell morphology associated with a migratory phenotype. Others have identified several genes with roles in cell migration that are directly transcriptionally regulated by p53. Even so, modulation of cell migration is not widely recognized as a p53 stress response. ^ In an effort to identify novel p53 target genes and expand our knowledge of the p53 transcriptional response, we performed Affymetrix gene expression analysis in p53-null PC3 prostate cancer cells following infection with a control virus or adenoviral construct expressing wild-type p53. Over 300 genes that had not been previously recognized as p53 target genes were identified. Of these genes, 224 were upregulated and 111 were downregulated (p<0.05). Functional over-representation analysis identified cell migration as a significantly over-represented biological function of p53. Further analysis identified two genes that are critical for the control of cell migration as potential p53 targets. One, hyaluronan mediated motility receptor (HMMR), has recently been shown to be a p53 target important for regulation of the cell cycle. Here, we show that HMMR is downregulated by p53 in several cell lines, and HMMR's regulation is dependent on the presence of the cdk inhibitor, p21, and histone deactelyase activity. The other gene, carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), itself a tumor suppressor, is shown here, for the first time, as a p53 direct target by ChIP analysis. We next determined the effect of p53 activation on cell migration and found that p53 significantly slows the rate of cell migration in Boyden chamber migration assays and digital videomicroscopy wound healing studies. Further, our studies established the specific roles of CEACAM1 and HMMR in cell migration and determine that loss of CEACAM1 and overexpression of HMMR independently contribute to increased cell migration. Taken together, these studies provide a direct mechanistic link between p53 to the regulatory control of specific target genes that mediate cell adhesion and migration. ^

Function of GCIP (CCNDBP1), a helix -loop -helix leucine -zip protein, in cell differentiation and tumorigenesis

Cell growth and differentiation are complex and well-organized processes in which cells respond to stimuli from the environment by carrying out genetic programs. Transcription factors with helix-loop-helix (HLH) motif play critical roles in controlling the expression of genes involved in lineage commitment, cell fate determination, proliferation and tumorigenesis. This study has examined the roles of GCIP (CCNDBP1) in cell differentiation and tumorigenesis. GCIP is a recently identified HLH-leucine zipper protein without a basic region like the Id family of proteins. However, GCIP shares little sequence homology with the Id proteins and has domains with high acidic amino acids and leucine-rich regions following the HLH domain like c-Myc. Here we firstly demonstrate that GCIP is a transcription regulator related to muscle differentiation program. Overexpression of GCIP in C2C12 cells not only promotes myotube formation but also upregulates myogenic differentiation biomarkers, including MHC and myogenein. On the other hand, our finding also suggests that GCIP is a potential tumor suppressor related to cell cycle control. Expression of GCIP was significantly down-regulated in colon tumors as compared to normal colon tissues. Overexpression of GCIP in SW480 colon cancer cell line resulted in a significant inhibition on tumor cell colony formation on soft agar assays while silencing of GCIP expression by siRNA can promote cell proliferation and colony formation. In addition, results from transgenic mice specifically expressing GCIP in liver also support the idea that GCIP is involved in the early stage of hepatocarcinogenesis and decreased susceptibility to chemical hepatocarcinogenesis. ^

Determination of the mechanical properties of corn grains and olive fruits required in DEM simulations

Discrete element method (DEM) is a numerical technique widely used for simulating the mechanical behavior of granular materials involved in many food and agricultural industry processes. Additionally, this technique is also a powerful tool to understand many complex phenomena related to the mechanics of granular materials. However, to make use of the potential of this technique it is necessary to develop DEM models capable of representing accurately the reality. For that, among some other questions, it is essential that the values of the microscopic material properties used to define the numerical model are accurately determined.

Código híbrido avanzado de motores de plasma de efecto Hall

La propulsión eléctrica constituye hoy una tecnología muy competitiva y de gran proyección de futuro. Dentro de los diversos motores de plasma existentes, el motor de efecto Hall ha adquirido una gran madurez y constituye un medio de propulsión idóneo para un rango amplio de misiones. En la presente Tesis se estudian los motores Hall con geometría convencional y paredes dieléctricas. La compleja interacción entre los múltiples fenómenos físicos presentes hace que sea difícil la simulación del plasma en estos motores. Los modelos híbridos son los que representan un mejor compromiso entre precisión y tiempo de cálculo. Se basan en utilizar un modelo fluido para los electrones y algoritmos de dinámica de partículas PIC (Particle-In- Cell) para los iones y los neutros. Permiten hacer uso de la hipótesis de cuasineutralidad del plasma, a cambio de resolver separadamente las capas límite (o vainas) que se forman en torno a las paredes de la cámara. Partiendo de un código híbrido existente, llamado HPHall-2, el objetivo de la Tesis doctoral ha sido el desarrollo de un código híbrido avanzado que mejorara la simulación de la descarga de plasma en un motor de efecto Hall. Las actualizaciones y mejoras realizadas en las diferentes partes que componen el código comprenden tanto aspectos teóricos como numéricos. Fruto de la extensa revisión de la algoritmia del código HPHall-2 se han conseguido reducir los errores de precisión un orden de magnitud, y se ha incrementado notablemente su consistencia y robustez, permitiendo la simulación del motor en un amplio rango de condiciones. Algunos aspectos relevantes a destacar en el subcódigo de partículas son: la implementación de un nuevo algoritmo de pesado que permite determinar de forma más precisa el flujo de las magnitudes del plasma; la implementación de un nuevo algoritmo de control de población, que permite tener suficiente número de partículas cerca de las paredes de la cámara, donde los gradientes son mayores y las condiciones de cálculo son más críticas; las mejoras en los balances de masa y energía; y un mejor cálculo del campo eléctrico en una malla no uniforme. Merece especial atención el cumplimiento de la condición de Bohm en el borde de vaina, que en los códigos híbridos representa una condición de contorno necesaria para obtener una solución consistente con el modelo de interacción plasma-pared, y que en HPHall-2 aún no se había resuelto satisfactoriamente. En esta Tesis se ha implementado el criterio cinético de Bohm para una población de iones con diferentes cargas eléctricas y una gran dispersión de velocidades. En el código, el cumplimiento de la condición cinética de Bohm se consigue por medio de un algoritmo que introduce una fina capa de aceleración nocolisional adyacente a la vaina y mide adecuadamente el flujo de partículas en el espacio y en el tiempo. Las mejoras realizadas en el subcódigo de electrones incrementan la capacidad de simulación del código, especialmente en la región aguas abajo del motor, donde se simula la neutralización del chorro del plasma por medio de un modelo de cátodo volumétrico. Sin abordar el estudio detallado de la turbulencia del plasma, se implementan modelos sencillos de ajuste de la difusión anómala de Bohm, que permiten reproducir los valores experimentales del potencial y la temperatura del plasma, así como la corriente de descarga del motor. En cuanto a los aspectos teóricos, se hace especial énfasis en la interacción plasma-pared y en la dinámica de los electrones secundarios libres en el interior del plasma, cuestiones que representan hoy en día problemas abiertos en la simulación de los motores Hall. Los nuevos modelos desarrollados buscan una imagen más fiel a la realidad. Así, se implementa el modelo de vaina de termalización parcial, que considera una función de distribución no-Maxwelliana para los electrones primarios y contabiliza unas pérdidas energéticas más cercanas a la realidad. Respecto a los electrones secundarios, se realiza un estudio cinético simplificado para evaluar su grado de confinamiento en el plasma, y mediante un modelo fluido en el límite no-colisional, se determinan las densidades y energías de los electrones secundarios libres, así como su posible efecto en la ionización. El resultado obtenido muestra que los electrones secundarios se pierden en las paredes rápidamente, por lo que su efecto en el plasma es despreciable, no así en las vainas, donde determinan el salto de potencial. Por último, el trabajo teórico y de simulación numérica se complementa con el trabajo experimental realizado en el Pnnceton Plasma Physics Laboratory, en el que se analiza el interesante transitorio inicial que experimenta el motor en el proceso de arranque. Del estudio se extrae que la presencia de gases residuales adheridos a las paredes juegan un papel relevante, y se recomienda, en general, la purga completa del motor antes del modo normal de operación. El resultado final de la investigación muestra que el código híbrido desarrollado representa una buena herramienta de simulación de un motor Hall. Reproduce adecuadamente la física del motor, proporcionando resultados similares a los experimentales, y demuestra ser un buen laboratorio numérico para estudiar el plasma en el interior del motor. Abstract Electric propulsion is today a very competitive technology and has a great projection into the future. Among the various existing plasma thrusters, the Hall effect thruster has acquired a considerable maturity and constitutes an ideal means of propulsion for a wide range of missions. In the present Thesis only Hall thrusters with conventional geometry and dielectric walls are studied. The complex interaction between multiple physical phenomena makes difficult the plasma simulation in these engines. Hybrid models are those representing a better compromise between precision and computational cost. They use a fluid model for electrons and Particle-In-Cell (PIC) algorithms for ions and neutrals. The hypothesis of plasma quasineutrality is invoked, which requires to solve separately the sheaths formed around the chamber walls. On the basis of an existing hybrid code, called HPHall-2, the aim of this doctoral Thesis is to develop an advanced hybrid code that better simulates the plasma discharge in a Hall effect thruster. Updates and improvements of the code include both theoretical and numerical issues. The extensive revision of the algorithms has succeeded in reducing the accuracy errors in one order of magnitude, and the consistency and robustness of the code have been notably increased, allowing the simulation of the thruster in a wide range of conditions. The most relevant achievements related to the particle subcode are: the implementation of a new weighing algorithm that determines more accurately the plasma flux magnitudes; the implementation of a new algorithm to control the particle population, assuring enough number of particles near the chamber walls, where there are strong gradients and the conditions to perform good computations are more critical; improvements in the mass and energy balances; and a new algorithm to compute the electric field in a non-uniform mesh. It deserves special attention the fulfilment of the Bohm condition at the edge of the sheath, which represents a boundary condition necessary to match consistently the hybrid code solution with the plasma-wall interaction, and remained as a question unsatisfactory solved in the HPHall-2 code. In this Thesis, the kinetic Bohm criterion has been implemented for an ion particle population with different electric charges and a large dispersion in their velocities. In the code, the fulfilment of the kinetic Bohm condition is accomplished by an algorithm that introduces a thin non-collisional layer next to the sheaths, producing the ion acceleration, and measures properly the flux of particles in time and space. The improvements made in the electron subcode increase the code simulation capabilities, specially in the region downstream of the thruster, where the neutralization of the plasma jet is simulated using a volumetric cathode model. Without addressing the detailed study of the plasma turbulence, simple models for a parametric adjustment of the anomalous Bohm difussion are implemented in the code. They allow to reproduce the experimental values of the plasma potential and the electron temperature, as well as the discharge current of the thruster. Regarding the theoretical issues, special emphasis has been made in the plasma-wall interaction of the thruster and in the dynamics of free secondary electrons within the plasma, questions that still remain unsolved in the simulation of Hall thrusters. The new developed models look for results closer to reality, such as the partial thermalization sheath model, that assumes a non-Maxwellian distribution functions for primary electrons, and better computes the energy losses at the walls. The evaluation of secondary electrons confinement within the chamber is addressed by a simplified kinetic study; and using a collisionless fluid model, the densities and energies of free secondary electrons are computed, as well as their effect on the plasma ionization. Simulations show that secondary electrons are quickly lost at walls, with a negligible effect in the bulk of the plasma, but they determine the potential fall at sheaths. Finally, numerical simulation and theoretical work is complemented by the experimental work carried out at the Princeton Plasma Physics Laboratory, devoted to analyze the interesting transitional regime experienced by the thruster in the startup process. It is concluded that the gas impurities adhered to the thruster walls play a relevant role in the transitional regime and, as a general recomendation, a complete purge of the thruster before starting its normal mode of operation it is suggested. The final result of the research conducted in this Thesis shows that the developed code represents a good tool for the simulation of Hall thrusters. The code reproduces properly the physics of the thruster, with results similar to the experimental ones, and represents a good numerical laboratory to study the plasma inside the thruster.

A contribution to the deterministic modelling of circadian rhythms in cell proliferation activity

This paper presents a deterministic continuous model of proliferative cell activity. The classical series of connected compartments is revisited along with a simple mathematical treatment of two hypotheses: constant transit times and harmonic Ts. Several examples are presented to support these ideas, both taken from previous literature and recent experiences with the fish Carassius auratus, developed at the Junta de Energía Nuclear, Madrid, Spain.

PIC computation of electron current collection to a moving bare tether in the mesothermal condition

In tethered satellite technology, it is important to estimate how many electrons a spacecraft can collect from its ambient plasma by a bare electrodynamic tether. The analysis is however very difficult because of the small but significant Geo-magnetic field and the spacecraft’s relative motion to both ions and electrons. The object of our work is the development of a numerical method, for this purpose. Particle-In-Cell (PIC) method, for the calculation of electron current to a positive bare tether moving at orbital velocity in the ionosphere, i.e. in a flowing magnetized plasma under Maxwellian collisionless conditions. In a PIC code, a number of particles are distributed in phase space and the computational domain has a grid on which Poisson equation is solved for field quantities. The code uses the quasi-neutrality condition to solve for the local potential at points in the plasma which coincide with the computational outside boundary. The quasi-neutrality condition imposes ne - ni on the boundary. The Poisson equation is solved in such a way that the presheath region can be captured in the computation. Results show that the collected current is higher than the Orbital Motion Limit (OML) theory. The OML current is the upper limit of current collection under steady collisionless unmagnetized conditions. In this work, we focus on the flowing effects of plasma as a possible cause of the current enhancement. A deficit electron density due to the flowing effects has been worked and removed by introducing adiabatic electron trapping into our model.

Genes encoding beta-mannanases in Brachypodium distachyon seeds have a role not only in cell wall softening upon germination sensu stricto but also during post-germinative reserve mobilization

En la coleorriza en semillas de Brachypodium son abundantes los mananos y estos van desapareciendo conforme progresa la germinación (entre 12-27 h), al mismo tiempo se observa un pico de actividad endo-beta-mananasa. Se ha establecido que de los 6 miembros de la familia MAN en B. distachyon 3 se expresan en el embrión en germinación y BdMAN3 también es abundante en la aleurona.

Overexpression of DNA polymerase β in cell results in a mutator phenotype and a decreased sensitivity to anticancer drugs

DNA polymerase β (pol β) is the most error prone of all known eukaryotic DNA polymerases tested in vitro. Here, we show that cells overexpressing pol β cDNA have acquired a spontaneous mutator phenotype. By measuring the appearance of mutational events using three independent assays, we found that genetic instability increased in the cell lines that overexpressed pol β. In addition, these cells displayed a decreased sensitivity to cancer chemotherapeutic, bifunctional, DNA-damaging agents such as cisplatin, melphalan, and mechlorethamine, resulting in enhanced mutagenesis compared with control cells. By using cell-free extracts and modified DNA substrates, we present data in support of error-prone translesion replication as one of the key determinants of tolerance phenotype. These results have implications for the potential role of pol β overexpression in cancer predisposition and tumor progression during chemotherapy.

Ubiquitous, heritable damage in cell populations that survive treatment with methotrexate

A permanent line of mouse embryo fibroblasts was treated with concentrations of the anticancer drug methotrexate (MTX) that left 20–50% surviving colonies. The surviving population initially multiplied at a much slower rate than controls after subculture in the absence of the drug, and required 9–12 days of serial subculture, with selective growth of the faster growing cells, to approximate the control rate. To determine the distribution of growth rates of cells in the original posttreatment populations, many single cells were isolated in multiwell plates immediately after the treatment period, and the resulting clones were serially subcultured. Most of the control clones underwent about 2 population doublings per day (PD/D). Almost all the survivors of MTX treatment multiplied at heterogeneously reduced rates, ranging from 0.6 PD/D to as high as control rates for a very few clones. They maintained the reduced rates through many subcultivations. The heritability of the reduced growth rates indicates that most cells that retain proliferative capacity after treatment with MTX carry random genetic damage that is perpetuated through many divisions of their progeny. Similar results have been described for cells that survive x-irradiation, and suggest random genetic damage is a common occurrence among cells in rapidly growing tissues that survive cytotoxic treatment. It also occurs in serial subcultures of cells that had been held under the constraint of confluence for extended periods, which suggests that the accumulation of random genetic damage to somatic cells during aging of mammals underlies the reduction of growth rate and function of the cells that characterizes the aging process.